Hi David,
What I am concerned about is how AddToBox would work. For example, let's
say that I want to create a box of 120Å x 60Å x 60Å. and fill it with tip3p
water molecules. If I now try to set the box dimensions by setting -X/Y/Z
AddToBox shows that the identifier -X is unknown.
My questions are,
1. How should I set up my box dimensions before I fill it up with the
required number of solvent molecules by -na flag?
2. How would the program understand that the water I add is tip3p since all
I am providing is a PDB file of a single water molecule with the -a flag?
Thank you for your time.
Regards,
Souvik
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 16 2020 - 13:00:02 PDT
